Modern tomography is the process of forming data models of three-dimensional objects by combining 2D projections of the object of interest typically obtained through the use of any kind of penetrating particle or wave. Tomography is a rapidly advancing imaging technology with broad applications in such varied fields such as but not restricted to medicine, dentistry, biology, environmental, toxicology, mineralogy, and electronics. Tomographic processes use various tools, such as x-ray systems, transmission electron microscopes (TEM), scanning transmission electron microscopes (STEM), and/or atom probe microscopes (APM) to obtain various types of information such as, for example, atomic structure and chemical analysis of the sample. A 3D tomography dataset is typically obtained by back projecting a series of 2D images acquired through the sample at different angles, or in the case of an APM by reconstructing a volume from a sequence of field-evaporated atoms striking a position-sensitive detector.
TEMs and STEMs allow observers to see extremely small features, on the order of nanometers, and allow analysis of the internal structure of a sample. For convenience, the reference to TEMs and STEMs will be indicated by the term “S/TEM” and references to preparing a sample for an S/TEM are to be understood to include preparing a sample for viewing in a TEM or a STEM. The sample must be sufficiently thin to allow many of the electrons in the beam to travel though the sample and exit on the opposite side. Thin S/TEM material and electronic samples are often seen as a thin section, referred to as a “lamella,” cut from a bulk sample material. Such lamellae are typically less than 100-200 nm thick, but for some applications a lamella must be considerably thinner. In S/TEM tomography, an electron beam is passed through the lamella and images acquired while the microscope stage is incrementally tilted. During this procedure the specimen rotates around an axis set to allow the feature of interest to remain in the field of view. A three-dimensional reconstruction of the original structure is then obtained. As the lamella is tilted, the angle between the beam (optical axis of the microscope) and the lamella surface decreases and the path length of the beam through the specimen increases, limiting the tilt angle than can be used and producing an undesirable “missing wedge effect” in the reconstructed volume. This missing information limits the resolution of the reconstructed volume and produces volumes that look stretch if observed from their side (conventionally along their z axis).
Some recent S/TEM tomography technique use pillar-shaped samples that are nominally cylindrical and contain a region of interest (ROI) desired to be examined by electron tomography. By “pillar” or “pillar-shaped” is meant any tomography sample such that a beam in a plane normal to the longitudinal axis of the pillar can pass through the sample from any direction. A pillar or pillar-shaped sample typically is roughly circularly symmetric (cylindrical or cone shaped). The use of pillar-shaped samples with a rotation holder offers two advantages: they allow a full rotation to eliminate missing wedge artifacts, and they provide a sample with a constant projection thickness at all rotation angles when rotated about the pillar's longitudinal axis (desirable for electron energy-loss spectroscopy (EELS) studies, for example).
In life sciences, techniques of adding fiducials like gold particles to the sample have proven useful to improve the quality of the 3D reconstruction on sectional type samples (mostly because the samples deforms locally under the beam during the acquisition).
In current methods for S/TEM tomography of materials science samples and semiconductor device samples, the alignment of pillar sample tilt-series relies mainly on cross-correlation between pairs of images through the tilt series. The alignment during the reconstruction phase has also been done using Discrete Algebraic Reconstruction Technique (DART) tomography by research groups in Belgium and Germany (IMEC, EMAT, University of Antwerp, IFW Dresden). Also, the current processes of aligning +/−90 degree tilt series from STEM tomography acquired on pillar samples has not become routine yet and is largely conducted manually by the operator, with low repeatability and little dedicated software features for alignment beyond cross-correlation.